No, not remotely starting from scratch.
The only thing that really changes is the game map as it's expanded with new areas, enemies, bosses, and such.
As the game has been worked on, I've made sure to set up any gameplay elements like enemies and items to essentially be drag and drop, there's a fairly simple work flow for rooms that lets me make new ones fairly fast and connect them to others, or adjust existing rooms in a matter of minutes.
To make a short summary; it's less starting from scratch and more just creating and putting in all the missing elements into a new map.
Building on top of what already exists.